Merge remote-tracking branch 'remotes/origin/develop' into fix-BIOPET-486

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

...rc/main/scala/nl/lumc/sasc/biopet/core/TemplateTool.scala

...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala

...ain/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala

...in/scala/nl/lumc/sasc/biopet/utils/BiopetExecutable.scala

...rc/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

...s/src/main/scala/nl/lumc/sasc/biopet/utils/Question.scala

.../main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

...ls/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

...ain/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala

.../src/main/scala/org/example/group/ExecutableExample.scala

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

...lumc/sasc/biopet/pipelines/gentrap/template/Gentrap.scala

...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

...iopet/pipelines/mapping/template/MultiSampleMapping.scala

...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

.../nl/lumc/sasc/biopet/pipelines/shiva/template/Shiva.scala